mirdeep2
alevin-fry
| mirdeep2 | alevin-fry | |
|---|---|---|
| 1 | 3 | |
| 129 | 153 | |
| 0.0% | 5.2% | |
| 2.5 | 7.2 | |
| 6 months ago | 2 months ago | |
| Perl | Rust | |
| GNU General Public License v3.0 only | BSD 3-clause "New" or "Revised" License |
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mirdeep2
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miRDeep2_core_algorithm.pl error
https://easyupload.io/hxygao
alevin-fry
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RNA VELOCITY
You can also get this information easily from the raw data using our alevin-fry tool. It produces a count matrix with spliced/unspliced/ambiguous counts that can easily be imported into python or R for velocity analysis. You can read more about alevin-fry here and check it out on github here. It's also easily installable via bioconda, and there's even a tool to simplify execution, called simpleaf. I'm happy to answer any questions you might have about using it!
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"Surpassing" Go & the near-future of Rust: in what domains will Rust succeed?
I think it depends on where in the space one is working. Our most recent tool, for example, is alevin-fry, which is for efficient preprocessing of single cell RNA seq data. Rust is the natural replacement for tools in the space that otherwise would have been in C++ (aligners, assemblers, large scale indexing, and things like RNA seq quantification and preprocessing). I view julia as more appropriate to replace tools currently existing in Python or R. There, I believe it can offer some substantial benefits. For our applications however, garbage collection is usually a non-starter.
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Our lab did a thing in rust (single-cell bioinformatics)
My lab has been trying to move most of our development over to rust (from C++). Our most recent paper presents a tool for single-cell and single-nucleus RNA-seq processing in rust https://rdcu.be/cIL35. The repo is https://github.com/COMBINE-lab/alevin-fry. It's one of our first "big" rust packages; so hopefully our design practices and rust skills will continue to improve.
What are some alternatives?
salmon - 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
pagoda2 - R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
OTTO - Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]
rust - Empowering everyone to build reliable and efficient software.
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
deno - A modern runtime for JavaScript and TypeScript.
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
AreWeRustYet - Awesome list of "Are We *thing* Yet" for Rust
miRPV - An Automated pipeline for miRNA identification and validation
alacritty - A cross-platform, OpenGL terminal emulator.
mixcr - MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.